NAMD is a parallel molecular dynamics code designed for
high-performance simulation of large biomolecular systems. NAMD
scales to hundreds of processors on high-end parallel platforms, as
well as tens of processors on low-cost commodity clusters, and also
runs on individual desktop and laptop computers. NAMD works with
AMBER and CHARMM potential functions, parameters, and file formats.
This article, directed to novices as well as experts, first
introduces concepts and methods used in the NAMD program,
describing the classical molecular dynamics force field, equations
of motion, and integration methods along with the efficient
electrostatics evaluation algorithms employed and temperature and
pressure controls used. Features for steering the simulation across
barriers and for calculating both alchemical and conformational
free energy differences are presented. The motivations for and a
roadmap to the internal design of NAMD, implemented in C++ and
based on Charm++ parallel objects, are outlined. The factors
affecting the serial and parallel performance of a simulation are
discussed. Finally, typical NAMD use is illustrated with
representative applications to a small, a medium, and a large
biomolecular system, highlighting particular features of NAMD, for
example, the Tcl scripting language. The article also provides a
list of the key features of NAMD and discusses the benefits of
combining NAMD with the molecular graphics/sequence analysis
software VMD and the grid computing/collaboratory software BioCoRE.
NAMD is distributed free of charge with source code at
www.ks.uiuc.edu.